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  "Title": "Copy Number study and Segmentation for multivariate biological\ndata",
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  "Date": "2021-11-20",
  "Author": "Yang Du",
  "Maintainer": "Yang Du <tooyoung@gmail.com>",
  "Description": "In this package, a Hidden Semi Markov Model (HSMM) and one\nhomogeneous segmentation model are designed and implemented for\nsegmentation genomic data, with the aim of assisting in\ntranscripts detection using high throughput technology like\nRNA-seq or tiling array, and copy number analysis using aCGH or\nsequencing.",
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  "Date/Publication": "2026-04-28 13:02:02 UTC",
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    "warning": 8,
    "note": 12
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
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    "email": "tooyoung@gmail.com",
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    "simSegData",
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